Publications by authors named "Maria Suntsova"

26 Publications

  • Page 1 of 1

Machine Learning Applicability for Classification of PAD/VCD Chemotherapy Response Using 53 Multiple Myeloma RNA Sequencing Profiles.

Front Oncol 2021 15;11:652063. Epub 2021 Apr 15.

I.M. Sechenov First Moscow State Medical University, Institute of Personalized Medicine, Moscow, Russia.

Multiple myeloma (MM) affects ~500,000 people and results in ~100,000 deaths annually, being currently considered treatable but incurable. There are several MM chemotherapy treatment regimens, among which eleven include bortezomib, a proteasome-targeted drug. MM patients respond differently to bortezomib, and new prognostic biomarkers are needed to personalize treatments. However, there is a shortage of clinically annotated MM molecular data that could be used to establish novel molecular diagnostics. We report new RNA sequencing profiles for 53 MM patients annotated with responses on two similar chemotherapy regimens: bortezomib, doxorubicin, dexamethasone (PAD), and bortezomib, cyclophosphamide, dexamethasone (VCD), or with responses to their combinations. Fourteen patients received both PAD and VCD; six received only PAD, and 33 received only VCD. We compared profiles for the good and poor responders and found five genes commonly regulated here and in the previous datasets for other bortezomib regimens (all upregulated in the good responders): , , , , and . Four of these genes are linked with known immunoglobulin locus rearrangements. We then used five machine learning (ML) methods to build a classifier distinguishing good and poor responders for two cohorts: PAD + VCD (53 patients), and separately VCD (47 patients). We showed that the application of FloWPS dynamic data trimming was beneficial for all ML methods tested in both cohorts, and also in the previous MM bortezomib datasets. However, the ML models build for the different datasets did not allow cross-transferring, which can be due to different treatment regimens, experimental profiling methods, and MM heterogeneity.
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http://dx.doi.org/10.3389/fonc.2021.652063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8083158PMC
April 2021

Gene Expression Signature of Endometrial Samples from Women with and without Endometriosis.

J Minim Invasive Gynecol 2021 Apr 8. Epub 2021 Apr 8.

OmicsWay Corp., Walnut, California (Drs. Suntsova and Buzdin and Mr. Nikitin, Garazha, Sorokin); Moscow Institute of Physics and Technology, Dolgoprudny (Dr. Buzdin and Mr. Sorokin); World-Class Research Center "Digital Biodesign and Personalized Healthcare", Sechenov First Moscow State Medical University (Drs. Suntsova and Buzdin and Mr. Sorokin), Moscow, Russia.

Study Objective: To develop a prototype of a complex gene expression biomarker for the diagnosis of endometriosis on the basis of differences between the molecular signatures of the endometrium from women with and without endometriosis.

Design: Prospective observational cohort study. Evidence obtained from a well-designed, controlled trial without randomization.

Setting: Department of reproductive medicine and surgery, A.I. Evdokimov Moscow State University of Medicine and Dentistry.

Patients: A total of 33 women (aged 32-38 years) were included in this study. Patients with and without endometriosis were divided into 2 separate groups. The group composed of patients with endometriosis included 19 living patients with endometriosis who underwent laparoscopic excision of endometriosis. The control group included 6 living patients who underwent laparoscopic excision of incompetent uterine scar after cesarean section, with both surgically and histologically confirmed absence of endometriosis and adenomyosis. An additional control/verification group included various previously RNA-sequencing-profiled tissue samples (endocervix, ovarian surface epithelium) of 8 randomly selected healthy female cadaveric donors aged 32 to 38 years. The exclusion criteria for all patients were hormone therapy and any intrauterine device use for more than 1 year preceding surgery, as well as absence of other diseases of the uterus, fallopian tubes, and ovaries.

Interventions: Laparoscopic excision of endometriotic foci and hysteroscopy with endometrial sampling were performed. The cadaveric tissue samples included endocervix and ovarian surface epithelium. Endometrial sampling was obtained from the women in the control group. RNA sequencing was performed using Illumina HiSeq 3000 equipment (Illumina, Inc., San Diego, CA) for single-end sequencing. Unique bioinformatics algorithms were developed and validated using experimental and public gene expression datasets.

Measurements And Main Results: We generated a characteristic signature of 5 genes downregulated in the endometrium and endometriotic tissue of the patients with endometriosis, selected after comparison with the endometrium of the women without endometriosis. This gene signature showed a capacity for nearly perfect separation of all 52 analyzed tissue samples of the patients with endometriosis (endometrial as well as endometriotic samples) from the 14 tissue samples of both living and cadaveric donors without endometriosis (area under the curve = 0.982, Matthews correlation coefficient = 0.832).

Conclusion: The gene signature of the endometrium identified in this study may potentially serve as a nonsurgical diagnostic method for endometriosis detection. Our data also suggest that the statistical method of 5-fold cross-validation of differential gene expression analysis can be used to generate robust gene signatures using real-world clinical data.
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http://dx.doi.org/10.1016/j.jmig.2021.03.011DOI Listing
April 2021

DNA repair pathway activation features in follicular and papillary thyroid tumors, interrogated using 95 experimental RNA sequencing profiles.

Heliyon 2021 Mar 13;7(3):e06408. Epub 2021 Mar 13.

I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia.

DNA repair can prevent mutations and cancer development, but it can also restore damaged tumor cells after chemo and radiation therapy. We performed RNA sequencing on 95 human pathological thyroid biosamples including 17 follicular adenomas, 23 follicular cancers, 3 medullar cancers, 51 papillary cancers and 1 poorly differentiated cancer. The gene expression profiles are annotated here with the clinical and histological diagnoses and, for papillary cancers, with gene V600E mutation status. DNA repair molecular pathway analysis showed strongly upregulated pathway activation levels for most of the differential pathways in the papillary cancer and moderately upregulated pattern in the follicular cancer, when compared to the follicular adenomas. This was observed for the BRCA1, ATM, p53, excision repair, and mismatch repair pathways. This finding was validated using independent thyroid tumor expression dataset PRJEB11591. We also analyzed gene expression patterns linked with the radioiodine resistant thyroid tumors (n = 13) and identified 871 differential genes that according to Gene Ontology analysis formed two functional groups: (i) response to topologically incorrect protein and (ii) aldo-keto reductase (NADP) activity. We also found RNA sequencing reads for two hybrid transcripts: one in-frame fusion for well-known translocation, and another frameshift fusion of oncogene with a new partner . The latter could probably support increased expression of truncated downstream from 4 exon out of 28. Both fusions were found in papillary thyroid cancers of follicular histologic subtype with node metastases, one of them () for the radioactive iodine resistant tumor. The differences in DNA repair activation patterns may help to improve therapy of different thyroid cancer types under investigation and the data communicated may serve for finding additional markers of radioiodine resistance.
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http://dx.doi.org/10.1016/j.heliyon.2021.e06408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7970325PMC
March 2021

Prognostic Role of Expression Status and Tumor-Related MicroRNAs Level in Association with PD-L1 Expression in Primary Luminal Non-Muscular Invasive Bladder Carcinoma.

Life (Basel) 2020 Nov 23;10(11). Epub 2020 Nov 23.

Department of Oncological Urology, Russian National Research Center of Radiology, 125284 Moscow, Russia.

Background: bladder cancer is one of the most common urinary tract malignancies. Establishment of robust predictors of disease progression and outcome is important for personalizing treatment of non-muscular invasive bladder carcinoma (NMIBC). In this study we evaluated association of PD-L1 expression with other prognostic biomarkers, such as expression of miRNA-145 and miRNA-200a, gene expression, and mutation status in tissue specimens of the luminal subtype of newly diagnosed high and low grade NMIBC.

Methods: twenty patients with primary luminal NMIBC were enrolled in the study. Tumor grade and risk level were determined in accordance with European Organization for Research and Treatment of Cancer (EORTC) guidelines and World Health Organization (WHO) classification. Neoplasm molecular subtype and PD-L1 expression level were assessed by immunohistochemistry. We used real-time PCR to evaluate the expression of microRNAs and . We detected hotspot mutations in codons 248 and 249 by Sanger sequencing.

Results: high grade primary luminal NMIBC showed comparatively higher expression of PD-L1 and microRNA-145 than a low grade tumor, whereas the latter had a higher expression and hotspot mutation rate. The tumor grade (HR = 571.72 [11.03-2.96] = 0.002), PD-L1 expression (HR = 2.33 [0.92-1.92] = 0.012), and expression (HR = 0.08 [0.17-0.42] = 0.003) were associated with relapse-free survival.

Conclusions: tumor grade in association with PD-L1 and expression can be considered as a complex predictor for primary luminal NMIBC progression.
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http://dx.doi.org/10.3390/life10110305DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7700587PMC
November 2020

Differences between human and chimpanzee genomes and their implications in gene expression, protein functions and biochemical properties of the two species.

BMC Genomics 2020 Sep 10;21(Suppl 7):535. Epub 2020 Sep 10.

Institute for personalized medicine, I.M. Sechenov First Moscow State Medical University, Trubetskaya 8, Moscow, Russia.

Chimpanzees are the closest living relatives of humans. The divergence between human and chimpanzee ancestors dates to approximately 6,5-7,5 million years ago. Genetic features distinguishing us from chimpanzees and making us humans are still of a great interest. After divergence of their ancestor lineages, human and chimpanzee genomes underwent multiple changes including single nucleotide substitutions, deletions and duplications of DNA fragments of different size, insertion of transposable elements and chromosomal rearrangements. Human-specific single nucleotide alterations constituted 1.23% of human DNA, whereas more extended deletions and insertions cover ~ 3% of our genome. Moreover, much higher proportion is made by differential chromosomal inversions and translocations comprising several megabase-long regions or even whole chromosomes. However, despite of extensive knowledge of structural genomic changes accompanying human evolution we still cannot identify with certainty the causative genes of human identity. Most structural gene-influential changes happened at the level of expression regulation, which in turn provoked larger alterations of interactome gene regulation networks. In this review, we summarized the available information about genetic differences between humans and chimpanzees and their potential functional impacts on differential molecular, anatomical, physiological and cognitive peculiarities of these species.
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http://dx.doi.org/10.1186/s12864-020-06962-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7488140PMC
September 2020

RNA Sequencing in Comparison to Immunohistochemistry for Measuring Cancer Biomarkers in Breast Cancer and Lung Cancer Specimens.

Biomedicines 2020 May 9;8(5). Epub 2020 May 9.

Institute of Personalized Medicine, I.M. Sechenov First Moscow State Medical University, Moscow 119048, Russia.

RNA sequencing is considered the gold standard for high-throughput profiling of gene expression at the transcriptional level. Its increasing importance in cancer research and molecular diagnostics is reflected in the growing number of its mentions in scientific literature and clinical trial reports. However, the use of different reagents and protocols for RNA sequencing often produces incompatible results. Recently, we published the Oncobox Atlas of RNA sequencing profiles for normal human tissues obtained from healthy donors killed in road accidents. This is a database of molecular profiles obtained using uniform protocol and reagents settings that can be broadly used in biomedicine for data normalization in pathology, including cancer. Here, we publish new original 39 breast cancer (BC) and 19 lung cancer (LC) RNA sequencing profiles obtained for formalin-fixed paraffin-embedded (FFPE) tissue samples, fully compatible with the Oncobox Atlas. We performed the first correlation study of RNA sequencing and immunohistochemistry-measured expression profiles for the clinically actionable biomarker genes in FFPE cancer tissue samples. We demonstrated high (Spearman's rho 0.65-0.798) and statistically significant ( < 0.00004) correlations between the RNA sequencing (Oncobox protocol) and immunohistochemical measurements for , and genes in BC, and for gene in LC; AUC: 0.963 for HER2, 0.921 for ESR1, 0.912 for PGR, and 0.922 for PDL1. To our knowledge, this is the first validation that total RNA sequencing of archived FFPE materials provides a reliable estimation of marker protein levels. These results show that in the future, RNA sequencing can complement immunohistochemistry for reliable measurements of the expression biomarkers in FFPE cancer samples.
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http://dx.doi.org/10.3390/biomedicines8050114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7277916PMC
May 2020

RNA sequencing profiles and diagnostic signatures linked with response to ramucirumab in gastric cancer.

Cold Spring Harb Mol Case Stud 2020 04 1;6(2). Epub 2020 Apr 1.

I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia.

Gastric cancer (GC) is the fifth-ranked cancer type by associated mortality. The proportion of early diagnosis is low, and most patients are diagnosed at the advanced stages. First-line therapy standardly includes fluoropyrimidines and platinum compounds with trastuzumab for HER2-positive cases. For recurrent disease, there are several alternative options including ramucirumab, a monoclonal therapeutic antibody that inhibits VEGF-mediated tumor angiogenesis by binding with VEGFR2, alone or in combination with other cancer drugs. However, overall response rate following ramucirumab or its combinations is 30%-80% of the patients, suggesting that personalization of drug prescription is needed to increase efficacy of treatment. We report here original tumor RNA sequencing profiles for 15 advanced GC patients linked with data on clinical response to ramucirumab or its combinations. Three genes showed differential expression in the tumors for responders versus nonresponders: , , and Of them, was up-regulated in the responders. Using the bioinformatic platform Oncobox we simulated ramucirumab efficiency and compared output model results with actual tumor response data. An agreement was observed between predicted and real clinical outcomes (AUC ≥ 0.7). These results suggest that RNA sequencing may be used to personalize the prescription of ramucirumab for GC and indicate potential molecular mechanisms underlying ramucirumab resistance. The RNA sequencing profiles obtained here are fully compatible with the previously published Oncobox Atlas of Normal Tissue Expression (ANTE) data.
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http://dx.doi.org/10.1101/mcs.a004945DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133748PMC
April 2020

Atlas of RNA sequencing profiles for normal human tissues.

Sci Data 2019 04 23;6(1):36. Epub 2019 Apr 23.

Omicsway Corp., 340S Lemon Ave, 6040, Walnut, 91789 CA, USA.

Comprehensive analysis of molecular pathology requires a collection of reference samples representing normal tissues from healthy donors. For the available limited collections of normal tissues from postmortal donors, there is a problem of data incompatibility, as different datasets generated using different experimental platforms often cannot be merged in a single panel. Here, we constructed and deposited the gene expression database of normal human tissues based on uniformly screened original sequencing data. In total, 142 solid tissue samples representing 20 organs were taken from post-mortal human healthy donors of different age killed in road accidents no later than 36 hours after death. Blood samples were taken from 17 healthy volunteers. We then compared them with the 758 transcriptomic profiles taken from the other databases. We found that overall 463 biosamples showed tissue-specific rather than platform- or database-specific clustering and could be aggregated in a single database termed Oncobox Atlas of Normal Tissue Expression (ANTE). Our data will be useful to all those working with the analysis of human gene expression.
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http://dx.doi.org/10.1038/s41597-019-0043-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6478850PMC
April 2019

Personalized prescription of imatinib in recurrent granulosa cell tumor of the ovary: case report.

Cold Spring Harb Mol Case Stud 2019 04 1;5(2). Epub 2019 Apr 1.

Stanford University School of Medicine, Stanford, California 94305, USA.

Ovarian cancer is the fifth leading cause of cancer-related female mortality and the most lethal gynecological cancer. In this report, we present a rare case of recurrent granulosa cell tumor (GCT) of the ovary. We describe the case of a 26-yr-old woman with progressive GCT of the right ovary despite multiple lines of therapy who underwent salvage therapy selection based on a novel bioinformatical decision support tool (Oncobox). This analysis generated a list of potentially actionable compounds, which when used clinically lead to partial response and later long-term stabilization of the patient's disease.
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http://dx.doi.org/10.1101/mcs.a003434DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6549576PMC
April 2019

Oncobox Bioinformatical Platform for Selecting Potentially Effective Combinations of Target Cancer Drugs Using High-Throughput Gene Expression Data.

Cancers (Basel) 2018 Sep 29;10(10). Epub 2018 Sep 29.

Laboratory of Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow 119991, Russia.

Sequential courses of anticancer target therapy lead to selection of drug-resistant cells, which results in continuous decrease of clinical response. Here we present a new approach for predicting effective combinations of target drugs, which act in a synergistic manner. Synergistic combinations of drugs may prevent or postpone acquired resistance, thus increasing treatment efficiency. We cultured human ovarian carcinoma SKOV-3 and neuroblastoma NGP-127 cancer cell lines in the presence of Tyrosine Kinase Inhibitors (Pazopanib, Sorafenib, and Sunitinib) and Rapalogues (Temsirolimus and Everolimus) for four months and obtained cell lines demonstrating increased drug resistance. We investigated gene expression profiles of intact and resistant cells by microarrays and analyzed alterations in 378 cancer-related signaling pathways using the bioinformatical platform Oncobox. This revealed numerous pathways linked with development of drug resistant phenotypes. Our approach is based on targeting proteins involved in as many as possible signaling pathways upregulated in resistant cells. We tested 13 combinations of drugs and/or selective inhibitors predicted by Oncobox and 10 random combinations. Synergy scores for Oncobox predictions were significantly higher than for randomly selected drug combinations. Thus, the proposed approach significantly outperforms random selection of drugs and can be adopted to enhance discovery of new synergistic combinations of anticancer target drugs.
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http://dx.doi.org/10.3390/cancers10100365DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6209915PMC
September 2018

Personalized prescription of tyrosine kinase inhibitors in unresectable metastatic cholangiocarcinoma.

Exp Hematol Oncol 2018 6;7:21. Epub 2018 Sep 6.

D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117198 Russia.

Background: Cholangiocarcinoma is an aggressive tumor with poor prognosis. Most of the cases are not available for surgery at the stage of the diagnosis and the best clinical practice chemotherapy results in about 12-month median survival. Several tyrosine kinase inhibitors (TKIs) are currently under investigation as an alternative treatment option for cholangiocarcinoma. Thus, the report of personalized selection of effective inhibitor and case outcome are of clinical interest.

Case Presentation: Here we report a case of aggressive metastatic cholangiocarcinoma (MCC) in 72-year-old man, sequentially treated with two targeted chemotherapies. Initially disease quickly progressed during best clinical practice care (gemcitabine in combination with cisplatin or capecitabine), which was accompanied by significant decrease of life quality. Monotherapy with TKI sorafenib was prescribed to the patient, which resulted in stabilization of tumor growth and elimination of pain. The choice of the inhibitor was made based on high-throughput screening of gene expression in the patient's tumor biopsy, utilized by Oncobox platform to build a personalized rating of potentially effective target therapies. However, time to progression after start of sorafenib administration did not exceed 6 months and the regimen was changed to monotherapy with Pazopanib, another TKI predicted to be effective for this patient according to the same molecular test. It resulted in disease progression according to RECIST with simultaneous elimination of sorafenib side effects such as rash and hand-foot syndrome. After 2 years from the diagnosis of MCC the patient was alive and physically active, which is substantially longer than median survival for standard therapy.

Conclusion: This case evidences that sequential personalized prescription of different TKIs may show promising efficacy in terms of survival and quality of life in MCC.
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http://dx.doi.org/10.1186/s40164-018-0113-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6127913PMC
September 2018

Acquired resistance to tyrosine kinase inhibitors may be linked with the decreased sensitivity to X-ray irradiation.

Oncotarget 2018 Jan 27;9(4):5111-5124. Epub 2017 Dec 27.

National Research Centre "Kurchatov Institute", Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow 123182, Russia.

Acquired resistance to chemotherapy and radiation therapy is one of the major obstacles decreasing efficiency of treatment of the oncologic diseases. In this study, on the two cell lines (ovarian carcinoma SKOV-3 and neuroblastoma NGP-127), we modeled acquired resistance to five target anticancer drugs. The cells were grown on gradually increasing concentrations of the clinically relevant tyrosine kinase inhibitors (TKIs) Sorafenib, Pazopanib and Sunitinib, and rapalogs Everolimus and Temsirolimus, for 20 weeks. After 20 weeks of culturing, the half-inhibitory concentrations (IC) increased by 25 - 186% for the particular combinations of the drugs and cell types. We next subjected cells to 10 Gy irradiation, a dose frequently used in clinical radiation therapy. For the SKOV-3, but not NGP-127 cells, for the TKIs Sorafenib, Pazopanib and Sunitinib, we noticed statistically significant increase in capacity to repair radiation-induced DNA double strand breaks compared to naïve control cells not previously treated with TKIs. These peculiarities were linked with the increased activation of ATM DNA repair pathway in the TKI-treated SKOV-3, but not NGP-127 cells. Our results provide a new cell culture model for studying anti-cancer therapy efficiency and evidence that there may be a tissue-specific radioresistance emerging as a side effect of treatment with TKIs.
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http://dx.doi.org/10.18632/oncotarget.23700DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5797037PMC
January 2018

A method of gene expression data transfer from cell lines to cancer patients for machine-learning prediction of drug efficiency.

Cell Cycle 2018 17;17(4):486-491. Epub 2018 Jan 17.

a National Research Centre "Kurchatov Institute" , Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow , Russia.

Personalized medicine implies that distinct treatment methods are prescribed to individual patients according several features that may be obtained from, e.g., gene expression profile. The majority of machine learning methods suffer from the deficiency of preceding cases, i.e. the gene expression data on patients combined with the confirmed outcome of known treatment methods. At the same time, there exist thousands of various cell lines that were treated with hundreds of anti-cancer drugs in order to check the ability of these drugs to stop the cell proliferation, and all these cell line cultures were profiled in terms of their gene expression. Here we present a new approach in machine learning, which can predict clinical efficiency of anti-cancer drugs for individual patients by transferring features obtained from the expression-based data from cell lines. The method was validated on three datasets for cancer-like diseases (chronic myeloid leukemia, as well as lung adenocarcinoma and renal carcinoma) treated with targeted drugs - kinase inhibitors, such as imatinib or sorafenib.
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http://dx.doi.org/10.1080/15384101.2017.1417706DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5927638PMC
September 2019

Gene expression and molecular pathway activation signatures of -amplified neuroblastomas.

Oncotarget 2017 Oct 28;8(48):83768-83780. Epub 2017 Jul 28.

D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.

Neuroblastoma is a pediatric cancer arising from sympathetic nervous system. Remarkable heterogeneity in outcomes is one of its widely known features. One of the traits strongly associated with the unfavorable subtype is the amplification of oncogene . Here, we performed cross-platform biomarker detection by comparing gene expression and pathway activation patterns from the two literature reports and from our experimental dataset, combining profiles for the 761 neuroblastoma patients with known amplification status. We identified 109 / 25 gene expression / pathway activation biomarkers strongly linked with the amplification. The marker genes/pathways are involved in the processes of purine nucleotide biosynthesis, ATP-binding, tetrahydrofolate metabolism, building mitochondrial matrix, biosynthesis of amino acids, tRNA aminoacylation and NADP-linked oxidation-reduction processes, as well as in the tyrosine phosphatase activity, p53 signaling, cell cycle progression and the G1/S and G2/M checkpoints. To connect molecular functions of the genes involved in -amplified phenotype, we built a new molecular pathway using known intracellular protein interaction networks. The activation of this pathway was highly selective in discriminating -amplified neuroblastomas in all three datasets. Our data also suggest that the phosphoinositide 3-kinase (PI3K) inhibitors may provide new opportunities for the treatment of the -amplified neuroblastoma subtype.
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http://dx.doi.org/10.18632/oncotarget.19662DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5663553PMC
October 2017

Data aggregation at the level of molecular pathways improves stability of experimental transcriptomic and proteomic data.

Cell Cycle 2017 Oct 21;16(19):1810-1823. Epub 2017 Aug 21.

a Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, National Research Centre "Kurchatov Institute" , Moscow , Russia.

High throughput technologies opened a new era in biomedicine by enabling massive analysis of gene expression at both RNA and protein levels. Unfortunately, expression data obtained in different experiments are often poorly compatible, even for the same biologic samples. Here, using experimental and bioinformatic investigation of major experimental platforms, we show that aggregation of gene expression data at the level of molecular pathways helps to diminish cross- and intra-platform bias otherwise clearly seen at the level of individual genes. We created a mathematical model of cumulative suppression of data variation that predicts the ideal parameters and the optimal size of a molecular pathway. We compared the abilities to aggregate experimental molecular data for the 5 alternative methods, also evaluated by their capacity to retain meaningful features of biologic samples. The bioinformatic method OncoFinder showed optimal performance in both tests and should be very useful for future cross-platform data analyses.
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http://dx.doi.org/10.1080/15384101.2017.1361068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5628641PMC
October 2017

Early stage of cytomegalovirus infection suppresses host microRNA expression regulation in human fibroblasts.

Cell Cycle 2016 Dec;15(24):3378-3389

e N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology of the Ministry of Health of the Russian Federation , Moscow , Russia.

Responses to human cytomegalovirus (HCMV) infection are largely individual and cell type specific. We investigated molecular profiles in 2 primary cell cultures of human fibroblasts, which are highly or marginally sensitive to HCMV infection, respectively. We screened expression of genes and microRNAs (miRs) at the early (3 hours) stage of infection. To assess molecular pathway activation profiles, we applied bioinformatic algorithms OncoFinder and MiRImpact. In both cell types, pathway regulation properties at mRNA and miR levels were markedly different. Surprisingly, in the infected highly sensitive cells, we observed a "freeze" of miR expression profiles compared to uninfected controls. Our results evidence that in the sensitive cells, HCMV blocks intracellular regulation of microRNA expression already at the earliest stage of infection. These data suggest somewhat new functions for HCMV products and demonstrate dependence of miR expression arrest on the host-encoded factors.
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http://dx.doi.org/10.1080/15384101.2016.1241928DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224468PMC
December 2016

Molecular pathway activation features of pediatric acute myeloid leukemia (AML) and acute lymphoblast leukemia (ALL) cells.

Aging (Albany NY) 2016 11;8(11):2936-2947

D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117198, Russia.

Acute lymphoblast leukemia (ALL) is characterized by overproduction of immature white blood cells in the bone marrow. ALL is most common in the childhood and has high (>80%) cure rate. In contrast, acute myeloid leukemia (AML) has far greater mortality rate than the ALL and is most commonly affecting older adults. However, AML is a leading cause of childhood cancer mortality. In this study, we compare gene expression and molecular pathway activation patterns in three normal blood, seven pediatric ALL and seven pediatric AML bone marrow samples. We identified 172/94 and 148/31 characteristic gene expression/pathway activation signatures, clearly distinguishing ALL and AML cells, respectively, from the normal blood. The AML and ALL cells differed by 139/34 gene expression/pathway activation biomarkers. For the 30 AML and 17 normal blood samples, we found 132/33 gene expression/pathway AML-specific features, of which only 7/2 were common for the adult and pediatric AML and, therefore, age-independent. At the pathway level, we found more differences than similarities between the adult and pediatric forms. These findings suggest that the adult and pediatric AMLs may require different treatment strategies.
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http://dx.doi.org/10.18632/aging.101102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5182073PMC
November 2016

In search for geroprotectors: in silico screening and in vitro validation of signalome-level mimetics of young healthy state.

Aging (Albany NY) 2016 09;8(9):2127-2152

Insilico Medicine, Inc, Research Department, Baltimore, MD 21218, USA.

Populations in developed nations throughout the world are rapidly aging, and the search for geroprotectors, or anti-aging interventions, has never been more important. Yet while hundreds of geroprotectors have extended lifespan in animal models, none have yet been approved for widespread use in humans. GeroScope is a computational tool that can aid prediction of novel geroprotectors from existing human gene expression data. GeroScope maps expression differences between samples from young and old subjects to aging-related signaling pathways, then profiles pathway activation strength (PAS) for each condition. Known substances are then screened and ranked for those most likely to target differential pathways and mimic the young signalome. Here we used GeroScope and shortlisted ten substances, all of which have lifespan-extending effects in animal models, and tested 6 of them for geroprotective effects in senescent human fibroblast cultures. PD-98059, a highly selective MEK1 inhibitor, showed both life-prolonging and rejuvenating effects. Natural compounds like N-acetyl-L-cysteine, Myricetin and Epigallocatechin gallate also improved several senescence-associated properties and were further investigated with pathway analysis. This work not only highlights several potential geroprotectors for further study, but also serves as a proof-of-concept for GeroScope, Oncofinder and other PAS-based methods in streamlining drug prediction, repurposing and personalized medicine.
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http://dx.doi.org/10.18632/aging.101047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5076455PMC
September 2016

Combinatorial high-throughput experimental and bioinformatic approach identifies molecular pathways linked with the sensitivity to anticancer target drugs.

Oncotarget 2015 Sep;6(29):27227-38

Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.

Effective choice of anticancer drugs is important problem of modern medicine. We developed a method termed OncoFinder for the analysis of new type of biomarkers reflecting activation of intracellular signaling and metabolic molecular pathways. These biomarkers may be linked with the sensitivity to anticancer drugs. In this study, we compared the experimental data obtained in our laboratory and in the Genomics of Drug Sensitivity in Cancer (GDS) project for testing response to anticancer drugs and transcriptomes of various human cell lines. The microarray-based profiling of transcriptomes was performed for the cell lines before the addition of drugs to the medium, and experimental growth inhibition curves were built for each drug, featuring characteristic IC50 values. We assayed here four target drugs - Pazopanib, Sorafenib, Sunitinib and Temsirolimus, and 238 different cell lines, of which 11 were profiled in our laboratory and 227 - in GDS project. Using the OncoFinder-processed transcriptomic data on ~600 molecular pathways, we identified pathways showing significant correlation between pathway activation strength (PAS) and IC50 values for these drugs. Correlations reflect relationships between response to drug and pathway activation features. We intersected the results and found molecular pathways significantly correlated in both our assay and GDS project. For most of these pathways, we generated molecular models of their interaction with known molecular target(s) of the respective drugs. For the first time, our study uncovered mechanisms underlying cancer cell response to drugs at the high-throughput molecular interactomic level.
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http://dx.doi.org/10.18632/oncotarget.4507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4694985PMC
September 2015

Molecular functions of human endogenous retroviruses in health and disease.

Cell Mol Life Sci 2015 Oct 18;72(19):3653-75. Epub 2015 Jun 18.

Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.

Human endogenous retroviruses (HERVs) and related genetic elements form 504 distinct families and occupy ~8% of human genome. Recent success of high-throughput experimental technologies facilitated understanding functional impact of HERVs for molecular machinery of human cells. HERVs encode active retroviral proteins, which may exert important physiological functions in the body, but also may be involved in the progression of cancer and numerous human autoimmune, neurological and infectious diseases. The spectrum of related malignancies includes, but not limits to, multiple sclerosis, psoriasis, lupus, schizophrenia, multiple cancer types and HIV. In addition, HERVs regulate expression of the neighboring host genes and modify genomic regulatory landscape, e.g., by providing regulatory modules like transcription factor binding sites (TFBS). Indeed, recent bioinformatic profiling identified ~110,000 regulatory active HERV elements, which formed at least ~320,000 human TFBS. These and other peculiarities of HERVs might have played an important role in human evolution and speciation. In this paper, we focus on the current progress in understanding of normal and pathological molecular niches of HERVs, on their implications in human evolution, normal physiology and disease. We also review the available databases dealing with various aspects of HERV genetics.
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http://dx.doi.org/10.1007/s00018-015-1947-6DOI Listing
October 2015

New bioinformatic tool for quick identification of functionally relevant endogenous retroviral inserts in human genome.

Cell Cycle 2015 ;14(9):1476-84

a Group for Genomic Regulation of Cell Signaling Systems ; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry ; Moscow , Russia.

Endogenous retroviruses (ERVs) and LTR retrotransposons (LRs) occupy ∼8% of human genome. Deep sequencing technologies provide clues to understanding of functional relevance of individual ERVs/LRs by enabling direct identification of transcription factor binding sites (TFBS) and other landmarks of functional genomic elements. Here, we performed the genome-wide identification of human ERVs/LRs containing TFBS according to the ENCODE project. We created the first interactive ERV/LRs database that groups the individual inserts according to their familial nomenclature, number of mapped TFBS and divergence from their consensus sequence. Information on any particular element can be easily extracted by the user. We also created a genome browser tool, which enables quick mapping of any ERV/LR insert according to genomic coordinates, known human genes and TFBS. These tools can be used to easily explore functionally relevant individual ERV/LRs, and for studying their impact on the regulation of human genes. Overall, we identified ∼110,000 ERV/LR genomic elements having TFBS. We propose a hypothesis of "domestication" of ERV/LR TFBS by the genome milieu including subsequent stages of initial epigenetic repression, partial functional release, and further mutation-driven reshaping of TFBS in tight coevolution with the enclosing genomic loci.
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http://dx.doi.org/10.1080/15384101.2015.1022696DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4612461PMC
February 2016

Human-specific endogenous retroviral insert serves as an enhancer for the schizophrenia-linked gene PRODH.

Proc Natl Acad Sci U S A 2013 Nov 11;110(48):19472-7. Epub 2013 Nov 11.

Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia.

Using a systematic, whole-genome analysis of enhancer activity of human-specific endogenous retroviral inserts (hsERVs), we identified an element, hsERVPRODH, that acts as a tissue-specific enhancer for the PRODH gene, which is required for proper CNS functioning. PRODH is one of the candidate genes for susceptibility to schizophrenia and other neurological disorders. It codes for a proline dehydrogenase enzyme, which catalyses the first step of proline catabolism and most likely is involved in neuromediator synthesis in the CNS. We investigated the mechanisms that regulate hsERVPRODH enhancer activity. We showed that the hsERVPRODH enhancer and the internal CpG island of PRODH synergistically activate its promoter. The enhancer activity of hsERVPRODH is regulated by methylation, and in an undermethylated state it can up-regulate PRODH expression in the hippocampus. The mechanism of hsERVPRODH enhancer activity involves the binding of the transcription factor SOX2, whch is preferentially expressed in hippocampus. We propose that the interaction of hsERVPRODH and PRODH may have contributed to human CNS evolution.
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http://dx.doi.org/10.1073/pnas.1318172110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3845128PMC
November 2013

Sense transcripts originated from an internal part of the human retrotransposon LINE-1 5' UTR.

Gene 2012 Dec 13;511(1):46-53. Epub 2012 Sep 13.

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow 117997, Russia.

L1 (LINE-1) is one of the most abundant families of human transposable elements. Full-length human L1 has an ~900 bp long 5' untranslated region (5' UTR) which harbors an internal promoter for the RNA polymerase II. It is generally accepted that the first 100 bp of the 5' UTR function as a "minimal promoter" which directs transcription of the entire LINE-1 unit from the extreme 5' terminus. We re-investigated promoter activities of the different DNA fragments that cover the whole L1 5' UTR in cultured human cells by using the luciferase reporter system. Analysis of both mRNA expression and luciferase activity levels indicated that the very important region for the effective transcription is located within the internal part of the L1 5' UTR between nucleotide positions +390 and +526. 5' RACE analysis revealed that in the context of the complete 5' UTR, this part drives mRNA synthesis both from the canonical 5'-terminal transcription start site (TSS) and from within the internal region. In the absence of the first 100 bp, the L1 5' UTR efficiently directed transcription from aberrant TSSs located within its 3' proximal part or the ORF1. Finally, we analyzed transcripts originated from endogenous (genomic) L1 elements and identified two novel TSSs located at positions +525 and +570. We propose a model in which the internal part (390-526) of the L1 5' UTR plays a key role for recruitment of transcription initiation complex, which then may be either positioned onto the 5' terminally located "minimal promoter", or used proximately to direct 5' truncated RNA copy. Intriguingly, this internal regulatory element substantially overlaps with the region of the L1 5' UTR that is known to drive transcription in the opposite direction suggesting the existence of a common core for the bidirectional transcription.
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http://dx.doi.org/10.1016/j.gene.2012.09.026DOI Listing
December 2012

Transcriptional regulation of human-specific SVAF₁ retrotransposons by cis-regulatory MAST2 sequences.

Gene 2012 Aug 15;505(1):128-36. Epub 2012 May 15.

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow 117997, Russia.

SVA elements represent the youngest family of hominid non-LTR retrotransposons. Recently, a human-specific subfamily (termed SVA(F1), CpG-SVA, or MAST2-SVA) was discovered representing fusion of the CpG island-containing exon 1 of the MAST2 gene and a 5'-truncated SVA. SVA(F1) includes at least 84 members, which suggests exceptionally high retrotransposition level. We investigated if the acquirement of the MAST2 CpG-island might play a role in the success of the SVA(F1) subfamily. We observed that in 16 samples representing seven human tissues, MAST2 was cotranscribed with the members of the SVA(F1) subfamily, but not with other retrotransposons. We found that the methylation status of the MAST2-derived sequences of SVA(F1) elements reversely correlates with the transcriptional activity of MAST2. The MAST2 sequence at the 5' end of SVA(F1) acts as a positive transcriptional regulator in human germ cells. Finally, in various testicular tissue samples we uncovered a transcriptional correlation of MAST2 with the human L1, Alu and SVA retrotransposons.
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http://dx.doi.org/10.1016/j.gene.2012.05.016DOI Listing
August 2012

nMETR: technique for facile recovery of hypomethylation genomic tags.

Gene 2012 Apr 13;498(1):75-80. Epub 2012 Feb 13.

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow 117997, Russia.

Genome-wide methylation studies frequently lack adequate controls to estimate proportions of background reads in the resulting datasets. To generate appropriate control pools, we developed technique termed nMETR (non-methylated tag recovery) based on digestion of genomic DNA with methylation-sensitive restriction enzyme, ligation of adapter oligonucleotide and PCR amplification of non-methylated sites associated with genomic repetitive elements. The protocol takes only two working days to generate amplicons for deep sequencing. We applied nMETR for human DNA using BspFNI enzyme and retrotransposon Alu-specific primers. 454-sequencing enabled identification of 1113 nMETR tag sites, of them ~65% were parts of CpG islands. Representation of reads inversely correlated with methylation levels, thus confirming nMETR fidelity. We created software that eliminates background reads and enables to map and annotate individual tags on human genome. nMETR tags may serve as the controls for large-scale epigenetic studies and for identifying unmethylated transposable elements located close to genomic CpG islands.
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http://dx.doi.org/10.1016/j.gene.2012.01.097DOI Listing
April 2012

Novel strong tissue specific promoter for gene expression in human germ cells.

BMC Biotechnol 2010 Aug 17;10:58. Epub 2010 Aug 17.

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.

Background: Tissue specific promoters may be utilized for a variety of applications, including programmed gene expression in cell types, tissues and organs of interest, for developing different cell culture models or for use in gene therapy. We report a novel, tissue-specific promoter that was identified and engineered from the native upstream regulatory region of the human gene NDUFV1 containing an endogenous retroviral sequence.

Results: Among seven established human cell lines and five primary cultures, this modified NDUFV1 upstream sequence (mNUS) was active only in human undifferentiated germ-derived cells (lines Tera-1 and EP2102), where it demonstrated high promoter activity (approximately twice greater than that of the SV40 early promoter, and comparable to the routinely used cytomegaloviral promoter). To investigate the potential applicability of the mNUS promoter for biotechnological needs, a construct carrying a recombinant cytosine deaminase (RCD) suicide gene under the control of mNUS was tested in cell lines of different tissue origin. High cytotoxic effect of RCD with a cell-death rate approximately 60% was observed only in germ-derived cells (Tera-1), whereas no effect was seen in a somatic, kidney-derived control cell line (HEK293). In further experiments, we tested mNUS-driven expression of a hyperactive Sleeping Beauty transposase (SB100X). The mNUS-SB100X construct mediated stable transgene insertions exclusively in germ-derived cells, thereby providing further evidence of tissue-specificity of the mNUS promoter.

Conclusions: We conclude that mNUS may be used as an efficient promoter for tissue-specific gene expression in human germ-derived cells in many applications. Our data also suggest that the 91 bp-long sequence located exactly upstream NDUFV1 transcriptional start site plays a crucial role in the activity of this gene promoter in vitro in the majority of tested cell types (10/12), and an important role--in the rest two cell lines.
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http://dx.doi.org/10.1186/1472-6750-10-58DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929213PMC
August 2010